A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.
This report has been generated by the bigbio/quantms analysis pipeline. For information about how to interpret these results, please see the documentation.
/home/runner/work/pmultiqc/pmultiqc/data
bigbio/quantms Methods Description
Suggested text and references to use when describing pipeline usage within the methods section of a publication.URL: https://github.com/bigbio/quantms
Methods
Data was processed using bigbio/quantms v1.5.0 (doi: 10.5281/zenodo.7754148) of the nf-core collection of workflows (Ewels et al., 2020), utilising reproducible software environments from the Bioconda (Grüning et al., 2018) and Biocontainers (da Veiga Leprevost et al., 2017) projects.
The pipeline was executed with Nextflow v24.10.5 (Di Tommaso et al., 2017) with the following command:
nextflow run bigbio/quantms -profile docker --custom_config_base /home/yueqx/Data_Disk/proteogenomics/quantms/test_dia/confs -c /home/yueqx/Data_Disk/proteogenomics/quantms/test_dia/confs/run_latest_dia.config
References
- Di Tommaso, P., Chatzou, M., Floden, E. W., Barja, P. P., Palumbo, E., & Notredame, C. (2017). Nextflow enables reproducible computational workflows. Nature Biotechnology, 35(4), 316-319. doi: 10.1038/nbt.3820
- Ewels, P. A., Peltzer, A., Fillinger, S., Patel, H., Alneberg, J., Wilm, A., Garcia, M. U., Di Tommaso, P., & Nahnsen, S. (2020). The nf-core framework for community-curated bioinformatics pipelines. Nature Biotechnology, 38(3), 276-278. doi: 10.1038/s41587-020-0439-x
- Grüning, B., Dale, R., Sjödin, A., Chapman, B. A., Rowe, J., Tomkins-Tinch, C. H., Valieris, R., Köster, J., & Bioconda Team. (2018). Bioconda: sustainable and comprehensive software distribution for the life sciences. Nature Methods, 15(7), 475–476. doi: 10.1038/s41592-018-0046-7
- da Veiga Leprevost, F., Grüning, B. A., Alves Aflitos, S., Röst, H. L., Uszkoreit, J., Barsnes, H., Vaudel, M., Moreno, P., Gatto, L., Weber, J., Bai, M., Jimenez, R. C., Sachsenberg, T., Pfeuffer, J., Vera Alvarez, R., Griss, J., Nesvizhskii, A. I., & Perez-Riverol, Y. (2017). BioContainers: an open-source and community-driven framework for software standardization. Bioinformatics (Oxford, England), 33(16), 2580–2582. doi: 10.1093/bioinformatics/btx192
Notes:
- The command above does not include parameters contained in any configs or profiles that may have been used. Ensure the config file is also uploaded with your publication!
- You should also cite all software used within this run. Check the "Software Versions" of this report to get version information.
Software Versions
Software Versions lists versions of software tools extracted from file contents.
| Group | Software | Version |
|---|---|---|
| ASSEMBLE_EMPIRICAL_LIBRARY | DIA-NN | 2.1.0 |
| CONVERT_RESULTS | quantms-utils | 0.0.23 |
| FINAL_QUANTIFICATION | DIA-NN | 2.1.0 |
| GENERATE_CFG | quantms-utils | 0.0.23 |
| INDIVIDUAL_ANALYSIS | DIA-NN | 2.1.0 |
| MSSTATS_LFQ | bioconductor-msstats | 4.14.0 |
| r-base | 4.4.2 | |
| MZML_STATISTICS | quantms-utils | 0.0.23 |
| PRELIMINARY_ANALYSIS | DIA-NN | 2.1.0 |
| SAMPLESHEET_CHECK | quantms-utils | 0.0.23 |
| SDRF_PARSING | sdrf-pipelines | 0.0.32 |
| THERMORAWFILEPARSER | ThermoRawFileParser | 1.3.4 |
| Workflow | Nextflow | 24.10.5 |
| bigbio/quantms | v1.5.0 |
bigbio/quantms Workflow Summary
- this information is collected when the pipeline is started.URL: https://github.com/bigbio/quantms
Input/output options
- export_decoy_psm
- true
- input
- /home/yueqx/Data_Disk/proteogenomics/quantms/test_dia/PXD026600.sdrf.tsv
- outdir
- /home/yueqx/Data_Disk/proteogenomics/quantms/results_dia
SDRF validation
- skip_factor_validation
- true
- use_ols_cache_only
- true
- validate_ontologies
- true
Protein database
- database
- /home/yueqx/Data_Disk/proteogenomics/quantms/test_dia/REF_EColi_K12_UPS1_combined.fasta
Database search
- allowed_missed_cleavages
- 1
- max_fr_mz
- 1500
- max_mods
- 2
- max_peptide_length
- 30
- max_pr_mz
- 950
- max_precursor_charge
- 3
- min_fr_mz
- 500
- min_peptide_length
- 15
- min_pr_mz
- 350
Modification localization
- luciphor_debug
- 0
PSM re-scoring (general)
- run_fdr_cutoff
- 0.10
PSM re-scoring (Percolator)
- description_correct_features
- 0
Consensus ID
- consensusid_considered_top_hits
- 0
- min_consensus_support
- 0
Isobaric analyzer
- quant_activation_method
- HCD
Protein Quantification (LFQ)
- feature_with_id_min_score
- 0.10
DIA-NN
- diann_normalize
- false
Statistical post-processing
- contrasts
- pairwise
Quality control
- enable_pmultiqc
- true
- pmultiqc_idxml_skip
- true
Institutional config options
- custom_config_base
- /home/yueqx/Data_Disk/proteogenomics/quantms/test_dia/confs
Generic options
- publish_dir_mode
- symlink
- trace_report_suffix
- 2025-07-22_10-44-58
Core Nextflow options
- configFiles
- N/A
- container
- [withLabel:diann:docker.io/library/diann-2.1.0]
- containerEngine
- docker
- launchDir
- /home/yueqx/Data_Disk/proteogenomics/quantms
- profile
- docker
- projectDir
- /home/yueqx/Data_Disk/proteogenomics/quantms/bigbio/quantms
- runName
- loquacious_wilson
- userName
- yueqx
- workDir
- /home/yueqx/Data_Disk/proteogenomics/quantms/work